The man in charge of overseeing The City’s $1.6 billion Central Subway project for the San Francisco Municipal Transportation Agency is departing for another transit agency: Caltrain.

Central Subway Program Director John Funghi will depart the SFMTA in February to lead Caltrain’s efforts to electrify their trains, the two agencies recently announced.

Funghi leaves as trains are set to roll through San Francisco’s Central Subway a year late and construction delays continue to plague Chinatown businesses.

The Caltrain Modernization Program will see the Caltrain corridor between San Francisco and San Jose become electric, a $1.9 billion program leveraging local, regional and federal funding to leave the days of diesel-hauled trains in the dust. It will also form the backbone of the soon-to-come high-speed rail project.

“I had a wonderful opportunity and I’m grateful for being a part of the Central Subway for as long as I did,” Funghi told the San Francisco Examiner on Friday. “Just having an opportunity to modernize Caltrain and modernize rail was just too good an opportunity to pass up.”

Given the Central Subway’s tenuous timeline, Funghi’s departure “is certainly a concern,” said Phil Chin, head of Chinatown TRIP, a transportation advocacy group.

“Ten years of knowledge is a heck of a lot to replace,” he added. “This is not a simple project.”

Funghi led the $1.6 billion Central Subway project as director since June 2006, which will see trains run from Chinatown through South of Market and to the Bayview. The project’s construction delays have grown after the San Francisco Examiner first reported them in July, from a 10-month delay to a full year.

Construction along Stockton Street led to some Chinatown businesses closing, their owners told the Examiner, and one of Mayor Ed Lee’s last acts in recent months was to direct more than $400,000 in mitigation funding and services to help ailing businesses endure the delay.

Independent audits of the SFMTA also warn that without strict adherence to delay-mitigation efforts, that Central Subway’s target date could slip from December 2019 to April 2020.

When asked who would step in for Funghi, SFMTA spokesperson Paul Rose said, “We will be accepting applications.”

Chin was surprised to hear that answer.

“That is not very reassuring,” Chin said, when told there is no immediate replacement for Funghi. “That is not very reassuring at all.”

Yet Funghi said he has a “good team” in place to help manage the project, and that more complex elements of it are now complete. The construction left, he said, is more akin to “typical building instruction.”

“It’s never a good time to leave a project,” he said, “but if there was a good time, this would be it.”

Funghi served the SFMTA for 18 years and is also a San Francisco native, according to an internal email sent by SFMTA Director of Transportation Ed Reiskin to SFMTA staff. “While we are losing a tremendous asset, Caltrain is inheriting a strong leader who understands the importance of world-class transportation for all,” Reiskin wrote.

In an interview in July, Funghi laid those delays at the feet of the construction contractor, Tutor Perini Corporation. Tutor Perini recently alleged that further delays may occur, in a series of documents given to the Board of Supervisors this month.